Additional methods for getting Chain type (protein, nucleic, etc)
Better logging in sifts #155
Better logging and some clean up in SeqRes2AtomAligner
Added a couple of methods to classes in contact package
Small bug fix: calling getCompounds explicitly at the end of parsing
Fixed important bug: ChainImpl.clone wasn't deep copying seqres groups
- also added a new test for checking of cross references so that cloning
bugs in the structure data model can be detected
More bug fixing in Structure/Chain/Group cloning: 
- parent references are now correctly reset
- compounds are now correctly deep-copied
Minor exception change
Some minor doc and deprecation changes
Bug fix: not including waters in contact calculation
Fixed issue in test
Adding @Override and @Deprecated tags where applicable

Most were added automatically using Eclipse
Fix #219

Convert GroupType to an enum.
Fixing an altLoc bug in mmcif parsing: parent chain wasn't set
- also added toPDB to Chain/ChainImpl
Improving StructureInterface.toPDB
Merge remote-tracking branch 'biojava/master'

Conflicts:
	biojava3-structure/src/main/java/org/biojava/bio/structure/Chain.java
	biojava3-structure/src/main/java/org/biojava/bio/structure/ChainImpl.java
	biojava3-structure/src/main/java/org/biojava/bio/structure/Compound.java
	biojava3-structure/src/main/java/org/biojava/bio/structure/HetatomImpl.java
	biojava3-structure/src/main/java/org/biojava/bio/structure/StructureImpl.java
Documentation improvements
Merge pull request #221 from sbliven/master

Fix #219: Make GroupType an enum